Modify render settings for all scenes using python
It works fine for me.

import bpy

for scene in bpy.data.scenes:
    scene.render.resolution_x = 1920
    scene.render.resolution_y = 1080
    scene.render.resolution_percentage = 100
    scene.render.use_border = False


Placing this in a file (test.py) and running blender with 

blender test.blend -P test.py


Opens blender with all the settings set to the values defined in the Python script, in both scenes.